Contacts of the helix formed by residues 132 - 145 (chain C) in PDB entry 2XMQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C ASP* 3.2 17.3 - - - -
131C VAL* 1.3 70.5 - - - +
133C ALA* 1.3 64.3 + - - -
135C ALA* 2.9 11.1 + - - +
136C TYR* 3.1 11.6 + - - +
155C ILE 3.0 14.5 + - - -
156C ASN* 4.0 19.5 - - - +
157C ILE* 4.8 1.4 - - - -
158C ASP 5.4 1.0 + - - -
186C HIS* 4.5 7.2 - - - -
223C TYR* 4.5 6.1 - - - -
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ASP* 3.2 7.8 + - - +
57C VAL* 3.9 11.0 - - + +
107C LEU* 4.2 7.9 - - + -
131C VAL 3.2 1.4 + - - -
132C GLY* 1.3 71.6 - - - -
134C GLY* 1.3 52.5 + - - +
136C TYR* 3.1 5.7 + - - +
137C ILE* 2.8 40.3 + - - +
219C TYR* 3.4 32.1 - - + +
223C TYR* 3.7 30.5 - - + -
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Residues in contact with GLY 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TYR* 3.4 33.9 - - - -
55C HIS 3.7 10.6 + - - -
130C GLY* 4.0 1.8 - - - -
131C VAL 2.8 11.6 + - - -
133C ALA* 1.3 76.0 - - - +
135C ALA* 1.3 58.0 + - - +
137C ILE* 3.2 3.6 + - - +
138C LEU* 2.9 32.9 + - - +
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Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C GLY* 3.8 15.7 - - - +
131C VAL 3.4 5.7 - - - +
132C GLY 2.9 10.1 + - - +
134C GLY* 1.3 73.8 - - - +
136C TYR* 1.3 66.2 + - - +
138C LEU* 3.5 0.6 + - - -
139C ALA* 3.0 20.1 + - - +
154C LEU* 3.3 20.6 - - + +
155C ILE 3.5 27.8 - - - +
157C ILE* 3.7 19.5 - - + -
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Residues in contact with TYR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU* 3.6 35.7 - - + -
108C ASP* 3.9 13.6 + - - -
132C GLY 3.1 10.7 + - - +
133C ALA* 3.5 10.1 - - - +
135C ALA* 1.3 76.3 - - - +
137C ILE* 1.3 60.6 + - - +
139C ALA* 3.1 4.2 + - - +
140C ARG* 2.9 47.0 + - + -
157C ILE* 3.8 12.0 - - + +
158C ASP 3.8 20.4 - - - +
159C PRO* 4.3 5.2 - - + -
223C TYR* 5.3 2.0 - - + -
226C ARG* 3.8 19.0 - - + -
227C ARG* 2.6 39.6 + - - +
229C LEU* 3.6 28.4 - - + +
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Residues in contact with ILE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TYR* 3.6 46.4 - - + -
107C LEU* 4.0 23.8 - - + +
110C LEU* 3.8 25.1 - - + -
111C ALA* 3.6 29.2 - - - +
114C ILE* 4.6 4.0 - - + -
133C ALA 2.8 25.5 + - - +
134C GLY* 3.4 5.2 - - - +
136C TYR* 1.3 74.4 - - - +
138C LEU* 1.3 52.6 + - - +
140C ARG* 3.2 2.9 + - - -
141C TYR* 2.7 34.5 + - - +
219C TYR* 3.7 9.4 - - - +
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 3.8 26.5 - - + +
54C TYR* 3.9 12.3 - - + -
114C ILE* 3.9 18.4 - - + -
126C ILE* 4.8 8.1 - - + -
128C GLY* 3.8 7.6 - - - -
129C VAL 3.1 48.0 - - - +
130C GLY* 3.5 7.2 - - - +
134C GLY 2.9 14.7 + - - +
135C ALA 4.0 3.4 - - - +
137C ILE* 1.3 76.5 - - - +
139C ALA* 1.3 57.3 + - - +
141C TYR* 3.5 6.6 - - + +
142C ALA* 3.0 26.5 + - - +
152C LEU* 4.1 17.0 - - + +
154C LEU* 4.6 4.5 - - + -
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Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ALA 3.0 18.5 + - - +
136C TYR 3.6 4.0 - - - +
138C LEU* 1.3 75.6 - - - +
140C ARG* 1.3 65.9 + - - +
142C ALA* 3.2 8.8 + - - +
143C LEU* 3.1 25.7 + - - +
152C LEU* 4.3 6.5 - - + -
154C LEU* 4.3 10.0 - - + +
157C ILE* 3.8 17.7 - - + -
229C LEU* 4.0 13.9 - - + -
231C PHE* 4.3 10.8 - - + -
239C LEU* 4.2 2.2 - - + +
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Residues in contact with ARG 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ASP* 2.8 29.6 + - - +
111C ALA* 3.7 17.9 - - + -
136C TYR* 2.9 31.0 + - + +
137C ILE* 3.7 3.6 - - - +
139C ALA* 1.3 76.3 - - - +
141C TYR* 1.3 65.8 + - - +
143C LEU* 3.0 40.1 + - - +
144C ASN* 3.2 31.6 + - - +
227C ARG* 3.4 26.2 - - - +
228C ASP 3.2 24.7 + - - -
229C LEU* 3.5 28.5 + - + +
237C ILE* 5.9 0.4 - - - +
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Residues in contact with TYR 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ALA* 3.6 25.7 - - + +
114C ILE* 3.7 32.3 - - + -
115C PRO* 3.7 11.5 - - + +
118C LEU* 3.4 18.2 - - + +
126C ILE* 3.9 18.4 - - + -
137C ILE 2.7 20.0 + - - +
138C LEU* 3.5 11.2 - - - +
140C ARG* 1.3 74.9 - - - +
142C ALA* 1.3 65.0 + - - +
144C ASN* 3.1 7.4 + - - +
145C HIS* 3.0 45.4 + + + +
148C THR* 2.7 31.8 + - - +
149C VAL* 3.5 17.9 - - + -
152C LEU* 6.4 0.2 - - + -
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU 3.0 16.5 + - - +
139C ALA 3.2 8.7 + - - +
141C TYR* 1.3 76.5 - - - +
143C LEU* 1.3 60.4 + - - +
146C PRO* 3.1 30.5 - - + +
149C VAL* 3.9 25.8 - - + -
152C LEU* 3.6 24.2 - - + -
239C LEU* 3.6 12.6 - - + -
241C CYS* 5.5 1.3 - - - -
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Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ALA 3.1 12.9 + - - +
140C ARG* 3.0 32.0 + - - +
142C ALA* 1.3 77.5 - - - +
144C ASN* 1.3 63.5 + - - +
146C PRO* 3.7 10.8 - - - +
229C LEU* 4.1 14.1 - - + +
231C PHE* 4.1 17.5 - - + -
237C ILE* 3.6 28.9 - - + -
238C THR 3.0 35.7 - - - +
239C LEU* 3.9 9.0 - - + -
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Residues in contact with ASN 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ASP 5.6 0.4 + - - -
111C ALA* 5.1 2.6 + - - +
112C ASP* 4.0 18.2 + - - -
140C ARG* 3.2 38.8 + - - +
141C TYR* 3.1 10.0 + - - +
143C LEU* 1.3 81.7 - - - +
145C HIS* 1.3 87.1 + - + +
146C PRO* 3.5 5.3 - - - +
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Residues in contact with HIS 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ALA 5.6 0.4 - - - -
112C ASP* 5.2 5.4 + - - -
115C PRO* 3.6 21.4 - - + +
141C TYR* 3.0 37.4 + + + +
142C ALA 3.4 3.1 + - - -
144C ASN* 1.3 109.5 + - + +
146C PRO* 1.3 67.6 - - - +
147C ASP* 3.2 6.3 - - - +
148C THR* 2.9 38.6 + - + +
149C VAL* 3.7 7.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il